Apocryphal
by Took.The.Midnight.Train
Summary: Richard Parker sent something that key to his research through a portal. Where did it go? What does it have to do with Peter? Only one way to find out. This is a Spider-man/Avengers Crossover. Slightly AU, main character is an OC. DISCLAIMER: I DO NOT OWN THE AVENGERS OR SPIDER-MAN
1. Prologue

**Prologue**

The moon sat comfortably on its apex in the black sky looking over a cement and steel fortress that lay hidden among rolling hills. It's light cast ominous shadows upon the secret facility that let off no light. Four towering brick walls surrounded the groups of buildings that made up the classified area. Clad with electrical barbed wire, the walls would have sent a shiver down the spine of any average civilian. Two shadows could be made out creeping alongside the south wall. Stealthily, they moved, cross stepping, almost dancing their way to the secured entrance; avoiding the pressure plates that would blow someone to bits if stepped on.

Continuing their odd dance, the shadows made their way to the mechanical steel gates that guarded the only entrance to the facility. When they had reached the intimidating, ominous barrier, the larger of the two figures pulled their right hand up to their left wrist to steady their arm. They then, carefully using a laser that was built into what looking like a watch, cut a six-foot rectangle through the steel door. Seeing that they had done a decent job, the larger figure motioned to their companion to lead the way into the secret area. The smaller figure adjusted the black hard covered backpack, which held a vital part of their mission, and pushed their way through the opening. The larger figure looked around once more and quickly followed their partner.

The two made their way to one of the smaller buildings right side of the main facility. When they got to the front glass doors that were rigged with heat sensors and a highly encrypted lock pad. Placing a circular device onto the lock pad, the figures stepped back and waited until they heard a slight beep from the device that signaled them that the door had been unlocked and the alarm system had been disabled. Using their gloved hand, the larger figure opened the reinforced glass door and held it for the smallest of the pair. Again, the smaller figure led the way, into the building. Waiting for their partner, the smaller figure took off the ski mask that hid their features from any security cameras or drones that may have flown overhead.

As the mask of the smaller person disappeared, their features were visible by the low lit blue light that lined the dry dement walls. Shoulder length raven hair that was pulled back into a ponytail revealed the features of a beautiful woman. A slightly rounded jaw, button nose, beautifully arching eyebrows and sparkling green eyes extenuated her slim, athletic figure. The larger figure followed suit. Brown hair, cold green eyes, a strong jaw and a hairline that was pulled back above his forehead, along with his well toned body, gave the man an aura of command. Eyes meeting, the man and woman simultaneously unhooked the guns that were strapped to their hips. Pointing their guns towards the ground, they proceeded deep into a labyrinth of hallways.

Upon making a flurry of turns through the dimly lit hallways, the couple finally reached their destination. A grey metal sliding door with an odd symbol upon it stood in front of them. The man stepped up to the computerized lock that protected the contents of the room that was guarded by the door. Holding up one of his gloved hands, his fingers flurried as they worked to break the code. While he was working at the door, the woman stood guard, ready to kill if someone were to find them.

A loud beeping noise rang through the cement building, emanating from the steel door. The pair remained calm, despite of the alarming sound. Pressing a button on the side of the panel, the man turned off the annoying noise. Grabbing a latch that was in the center if the door, the man manually pulled the door open, entering immediately; checking the hallway one more time, the woman cautiously followed. Once the door was closed, the man went straight towards the largest piece of equipment in the room. Standing, much like a centerpiece at an art exhibit, the machine was nothing ordinary. Its base was four square feet of white metal, which held up a slight elevated platform the same size. On each side of the platform was a cylindrical rod that curved up to seven feet. Neatly spaced up the rods were smaller prongs that looked as if they emitted some for of electrical charge. A flurry of wires came out of the side of the machine and hooked up to a table-top key board and automated screen ten feet away; it was here that the man stood, furiously typing.

His partner was a few feet behind him, knelt by the door with the hard-covered backpack on the ground in front of her. Pulling the zipper open, she reached into the backpack and pulled out a clear, peanut shaped object. A foot long and seven inches in diameter at the ends and five in the middle, the object resembled that of a case. Two black clasps held the case closed. On the farther end of the case, a black rectangular jutted out from the bottom of the large peanut. A tube attached itself between the box and the very top of the case. A large white O could be read on the outside of the black box.

Picking up the case and holding it in her hands, the woman stroked the front of it, her eyes gazing down into the hazy glass-like material with a mixture of love and sadness. Her eye were drawn away from the case when a loud humming echoed throughout the room, letting her, and her partner know that the machine was ready for use. Walking over to the man, case still in hand, the woman started to feel her eyes swell with tears that threatened to overflow.

Looking up from the table, the man saw the pain and sorrow that he felt emanating in his partners eyes. Pressing a few more buttons, he walked over to her, his arms outstretched, offering a loving embrace. Swiftly moving into his arms, she grasped the case to her chest and let out a choked sob. Soothingly rubbing her back, the man kissed the top of her head before nestling his face into her hair, pulling her tighter yet into his chest.

"It's for the best Mary, it's the only way to keep her safe." The man whispered into her hair. Letting out another sob, Mary tried to pull herself together long enough to reply.

"Why did you have to do this Richard, why does it have to be this way?" She choked out between sobs. Richard did not answer, but he could feel the guilt build up inside of him. Letting go of Mary, Richard walked back to the keyboard, making some final preparations.

Upon finishing his prep work, Richard turned to Mary, silently telling her to put the case on top of the platform in the middle of the machine. Mary merely clutched the case tighter to her bosom, shaking her head in silent defiance. Richard's shoulders seemed to deflate as he walked over to Mary, holding out his arms, beckoning her to give him the case. Her arms shaking, she stretched her arms forward, giving the object to Richard. Crumpling to the floor in a wrenching heap, Mary could not find the energy to move.

After placing the capsule on the platform, Richard moved back to the keyboard, pressing a few more buttons and turning some dials. His right hand moved to a blue square button, that when pressed, would seal fate forever. Looking over sadly to Mary, who could be heard crying softly "My baby, my little girl," Richard felt the knot in his stomach twist and tighten. His finger barely twitched as he pressed the button.

A flash of light emanated from the machine, blinding both Richard and Mary. When the light had cleared, the capsule was gone, and the ghost of a whisper could be heard on the slight breeze that the machine had left.

"I did it to protect her."

**(A/N): Hi,**

**Okay so this is my first multi chapter, actually-has-a-plot, fic on here. I will try to update weekly.**

**Please let me know what you think of the story. **


	2. Chapter 1

**Chapter 1**

Kathlyn Jane Thomson stood at the edge of the ship, smiling as she felt the breeze of the ocean whip her sandy hair around her face, masking her vision slightly. Pulling the purple windbreaker she was wearing tighter around her slender frame, she refused to think of why she was crossing back to the mainland. Instead, she attempted to enjoy the fresh air, and remember the wonderful time that she had had while she had been living with her aunt.

Two years back, Kathlyn and her parents had had a disagreement about a certain boy that Kathlyn had been interested in. They were worried about their 'baby girl' so they sent her to live with her aunt, who had been perfectly healthy at the time. Her aunt, Maggie, lived on Vancouver Island, off the coast of British Columbia, Canada. Kathlyn had had the time of her life. The Island was beautiful, and her aunt lived right on the ocean. Kathlyn had made friends at the local high school and always ended up spending the afternoons, that when the water was somewhat decent, and the sun was kind of shinning, on the rock filled beach. Then, her freedom from her overbearing parents came to an end when Maggie had become very sick. She refused to see the doctor saying that it was fine, just a cold. It was not a cold. Kathlyn was not told what Maggie had contracted, but it had been fatal. Kahtlyn stayed after the funeral to clean out the house, wanting to stay away from her parent as long as possible.

Now she stood on the ferry, headed back home to Kamloops, an annoying city of 90, 000 that was not the ideal place to grow up. Boring as hell for a teenager, Kamloops was a horrid place in her mind. Sure, it was big enough that she didn't have to worry about small ton gossip, but it small enough that you could become bored out of your mind in an instant. Kamloops was a very arid climate, and in the summers, when there were forest fires, all the smoke decided to accumulate in the valley of the city, leaving a haze and making it impossible to breathe.

Kathlyn knew that her days of freedom had come to an end. She had said goodbye to her friends that morning and was now headed to Vancouver via ferry. Her parents were waiting on the other side. She had imagined their reunion for a couple of weeks. Her mother would smile and hug her tightly, tears growing in her eyes. She would say how proud she was of Kathlyn and how much she loved her. Her father would offer a quick hug, smile and offer to take her bags. They would get in the car and her mother would start to rave about all that Kathlyn had missed while she was away. Kathyn would stare out the window, then plug into her ipod and listen to music, ignoring her parents for the next four hours of driving.

Kathlyn was adopted. Her parents had not been able to conceive, so she was the result. Her birth parents had been killed in a plane crash. Her adopted parents had always been far too protective of her. She had had a sheltered childhood, so when the first boy came round when she was fourteen, she got into a bit of trouble. Kathlyn had been sent away, _"for her own safety." _She had matured over the last two years, and now, at the age of sixteen, Kathlyn could not wait to leave Kamloops, and her parents behind for good.

* * *

Peter swung from building to building, feeling free. Bending, pulling, releasing; he was flying. Mindlessly following the rhythm that he had created, Peter enjoyed the peace. It was around dinnertime and he had been out all afternoon, going around the city, watching out for any disturbances. There hadn't been much, but lately there wasn't. After the alien attack three weeks previous, the city had quieted and crime was at an all-time low. The alien attack was crazy, and he had been able to help a little, but he knew that the group of heroes, _The Avengers_ had done most of the work.

Though Peter was grateful to the super group, he was somewhat annoyed with them; where had they been when the Lizard had attacked the city? Did they only care when the entire world was in danger, and not a whole city. He continued onward, deciding to call it a night and go home. For once, he had time to kill, and might be able to get some homework done.

As Peter slunk down into as alley where he had hid his backpack, he did not notice the woman on her cell phone, walking a small puff-ball of a dog. Wearing sunglasses during a rainy day, and clad in a fur coat while the temperature was relatively warm, it was a wonder she didn't stand out. Seeming to be talking on her cell phone in a hushed voice, the woman turned slightly, barely making out Peter's shadow amongst those of the alley.

Speaking into the receiver, she said "Target has been sighted."

* * *

**(A/N) **

**Hi, **

**So I know that I said I would update regularly, but it's near exam time so that will be a lie. I will try to update soon, but I don't have any specific time frame to give.**

**Here is a but of background information on the chapter. Kamloops is an actual city, it's located four and a half ish hours north east of Vancouver BC CANADA. It's a lovely city of you plan to visit, or if you are raising a family, but as a teen, it's bad. There is nothing to do. Vancouver Island, if you have not been there is GOERGEOUS, you have to go sometime. Tere's this awesome town called Chemainus and they have this amazing candy shop called Hansel and Gretel's Candy Shop, and they sell the BEST bonbons around. There's also this Christmas Store across the street from the Candy shop, and they have the most unique ornaments.**

**Anyway so thanks for reading, now please review :P**

**TTYL**


	3. Chapter 2

**Chapter 2**

Peter emerged from the dark alley, blending easily with the busy afternoon crowd that made up Manhattan. Behind him, the woman with the fur coat walking her dog ducked into one of the many stores that lined the street. She tied the dog up outside; knowing that one of the other operative would pick it up. She shed her fur coat to reveal a plain white V-neck t-shirt that accentuated her curves. She was wearing a pair of straight leg jeans that looked relatively well worn. Slipping out of the store, she wove her way easily through the busy crowd; it took her less than ten seconds to locate the brown mop of hair that belonged to Peter Parker.

Stalking the teenage boy with the used backpack and the hoodie, the woman was always vigilant of her surroundings. Many years of training had taught her to never stay focused on one thing too long, but to be aware of everything simultaneously. Some scientists would say that this was impossible, but then most scientists were not word class operatives.

The woman followed Peter down a set of busy stairs that led to the subway. Making sure to not lose sight of him, she watched as he walked over to the platform, waiting for a train that would take him home. When the train finally arrived, it screeched to a halt, the doors slid open to reveal a flurry of people in business suits. Pushing against the flow of bodies, the woman barely managed to get on the train. Peter found a seat quickly and immediately plugged into his iPod, trying to drown out the noises of the world. Sitting across from him, the woman pretended to read something on the cell phone that had been given to her.

After much time, Peter stood to get off. After about half an hour more, they reached his house. It was similar to the rest on the street. A quaint two story building with a small stoop. Standing on the other side of the street, the woman watched at Peter entered the house, closing the door with the glass window behind him. Turning away from the row of houses opposite her, she picked up her phone and dialed a number. A deep voice answered.

"Black Widow, report."

"Subject is as we thought. Residence in 738 Winter Garden Drive. Subject is in fact Peter Parker sir. Would you like contact to be made?" There was slight silence on the other end.

"Not yet. Return to base and await further instructions."

* * *

Kathlyn flopped on her bed, her curly hair spreading over the pastel floral spread. Staring at her ceiling for a minute, she let all her emotions swell up in her. Reaching above her head, she grabbed a pillow; pulling it to her face, she screams loudly, hoping that the pillow would mute her anger.

She had returned home less than a half hour ago. She had hid in her room nearly immediately, refusing to come out. There were so many times when she thanked her stars that school was over. If she had had to return to school, she would have screamed. Kahtlyn lay, thinking about how she could avoid her parents all summer. She had no friends in town, not really, but she loved to head downtown and spend the day there. She loved to go down to the park by the river and enjoy the serene flow of the water. Her parents worked from early until late, so she wouldn't have to see them too often.

Rolling up, Kahtlyn made her way over to her bookshelf that was beside her bed. She looked over the small collection that seemed like so many. Picking up one of her favorite books, she curled back onto her bed and immerged herself into a different land, one of adventure and romance, where anything could happen. Hours passed before Kahtlyn finally put down the book. Listening for a moment, she heard nothing outside her door. She thought this weird, as it seemed early. She grabbed her phone off her covers and got up from the bed. Her feet took her to the door as she checked the time on her phone. 11:27 pm, is what the illuminated clock read. Kathlyn froze, her hand suspended above the door knob. How had she missed the time. She decided to head to bed, and hope that tomorrow would be a better day.

The next day, Kathlyn woke up late. Both her parents went to work long before she was awake. After cleaning the kitchen and unpacking her things, she decided to go for a walk so that she could sort through her emotions. She was determined to not act like a total brat all summer. There was a small pond near her house, and Kathlyn had often gone there to escape when she was younger. Sitting on a bench under a willow tree, Kathlyn enjoyed the silence of this place. No one ever came here, it was her personal haven.

All of a sudden, Kahtlyn felt a tug just above her navel. It felt as if an invisible string was pulling her backwards. SHe started to panic as her world started to change. Bit by bit, the world started to go white, as if it was being erased. Pieces of the scenery would disappear as if they were merely photo shopped. Kathlyn felt as though she was moving, yet it did not seem so. he world kept fading as she was pulled into a tunnel of white eventually everything disappeared and Kathlyn was left with nothing.

* * *

**(A/N)**

Hello

I know this chapter is a bit shorter but I promise that things will speed up soon.

So, tell me what you think

Thnx


	4. Chapter 3

**Chapter 3**

Nick Fury, director of SHIELD sat at a desk, somewhere with the depths of the SHIELD Heli Carrier. The room was a plain cement cube, with only a glass door to ornament the walls. The desk was made of metal, stainless steel. A laptop that belonged to non-other than the director sat open, but the screen was black. From a quick glance around the room, anyone could see that it was rarely used. Leaning back into his chair, Fury let out a groan as he rubbed his face with his calloused and scarred hands. He had just received the confirmation of the identity of the vigilante, Spider-Man. He had suspected for some time that the once mysterious hero had been the son of his deceased friend.

Richard had been a good operative, and a good friend, and he would have made a fantastic father, but he had had too many secrets he still did. Fury had suspected that secrets would be his downfall, he just hoped that they the tradition would not be passed onto his son.

SHIELD had been watching over Peter since the years of his parents' death. They did not keep a tight eye on the boy, but they would check in every now and again to make sure that the kid was still alive and safe. Fury had done this as a favor. He knew that Richard and Mary had made many enemies whilst working as agents. They had been some of the best, and the Director knew that the only thing that kept them from continuing their life of danger and adventure was having a family. When Mary had become pregnant with Peter, the couple had hoped that they could leave their life of secrecy behind them, but that didn't happen. Fury was one of the few who knew the truth of their death, and he would never tell a soul.

He turned his mind back to the matter at hand. He was torn. He wanted to let Peter be, and hopefully continue looking after the kid from a distance, but now that his alter ego was confirmed, Fury knew that this would soon be futile. After the Lizard incident, Fury knew that Spider-Man would need help. Originally, he had hoped that the masked man was old enough and had enough experience that he would not need too much help, but a teenager was a whole different story. Nick knew that Peter would need someone to turn to, he also knew that it would take quite a bit to convince the boy. Peter was strong willed and always wanted to look after those he loved, but he needed some looking after to.

Finally after weighing the pros and cons of the whole situation, the Director of Strategic Homeland Intervention, Enforcement and Logistics decided on a plan to bring the super boy under their care, not just for support, but for research as well. Fury wanted to know the how's and why's of this teenage hero.

Just as Fury was about to inform some people about his plan, he received a phone call. Reaching into his jacket pocket, he pulled out his phone to answer.

"Sir, Head scientist Andrews here, we have a situation, we found something," the voice on the other line said after Fury had answered.

"What is it Andrews, why is it so important, I have other things that need to be done" Fury said, losing patience. Though he was the director, he had more important things to do than oversee every little thing that went on.

"Trust me sir, you want to see this." Andrews insured.

"Fine" Fury grumbled before hanging up.

Walking out of his office, he made his way toward the main lab of the Heli Carrier. Winding his way there, he couldn't help but feel slightly giddy. He needed something to take his mind off the Spider-Man case, and something unknown could definitely do the trick.

He reached the white glass door that led to the lab. Sliding his access card over a panel on the left wall, he would not have expected what was waiting for him on the other side. Entering the room, with a stoic face, moving closer to the operating table that was in the middle of the room, Fury, for once, was speechless.

* * *

**(A/N) **

So here is another shorter chapter, I wanted the story to pick up a but here, and Voila. Please don't kill me for the cliffy, but I need to keep you reading somehow, right ;)

What do you think is on the operating table?

Please please please review and help me improve my writing.

Thnx


	5. Chapter 4

Director Fury stood before the operating table in the main lab of the SHIELD Heli Carrier thousands of feat above the ground. His mind was racing, trying to understand, but could not grasp why, or how. What he beheld with his eyes should not exist. He had heard rumors, but did not fathom that they were true. Quickly snapping out of his trance, he looked sharply at Doctor Andrews, the head researcher of SHIELD.

"How is this possible Andrews?" He asked, trying to keep the shock out of his voice. Andrews looked over the object of their scrutiny.

"I told you sir, I don't know. It just happened. We were notified of the incident and we picked this up." Andrews replied.

"Well figure it out." Fury said before he stormed out of the room.

* * *

Tony Stark was bored. Since the Mandarin incident, much had changed. He had had the arc reactor in his chest removed along with the shrapnel from so long ago. All of his suits were gone, and he had gotten help for his PTSD from the Chitauri incident. Things had smoothed out between him and Pepper and he even had a new house under way. The only problem was that he was bored.

He had not had anything to do. Pepper was always busy with the company; he was not allowed to through the blueprints for the new house, and he was forbidden to make any new Iron Man suits until he was given the all clear from SHIELD. They were worried that he would get cocky and end up making enemies that wanted the planet destroyed.

Since the Chitauri incident, SHIELD had basically thrown the Avengers aside. Technically the initiative never existed in the first place, and Fury seemed all too happy to let the members of the circle lay low, though Tony had done the opposite.

To be honest, he felt lonely. Steve was who knows where, grieving over the fact that he would not see his old friends from the War. Thor was in another dimension doing goodness know what. Romanov and Barton were off on top-secret missions, and Banner was doing boring science-y stuff, the kind that made Tony fall asleep. Tony had decided to go to New York for a bit, to clear his head and hopefully find something that didn't bore him to death, and sure enough, he had.

The Lizard incident had happened shortly after the Chitauri, right when Manhattan was starting to feel better about world destruction. The city had been cleared out and life was easing its way back nearly seamlessly into the constant routine of the dazzling city. Out of nowhere, a Lizard man, who was one of OSCORPs top researchers, nearly turned millions of people into ugly green rage monsters, not unlike the Hulk. SHIELD had done nothing about the situation, as far as Tony knew, saying that it was taken care of; and sure enough, it was.

He had immediately become nearly obsessed with finding out who and what Spider-Man was. There were so many questions to be answered; where did he come from, how did he get his powers, was he a mutant, and most importantly, who was he. Tony had pulled up every bit of information he could find about this vigil ante, who had jumped from a personal vendetta to saving the city nearly over night. Newspaper clippings, police reports, online theories, everything. There had been a lot of speculation already done about the new hero. Some made Tony wonder about the future of the human race, others made him thankful that not everyone was dull and stupid. Most of the people online thought that Spider-Man was either a mutant, or an alien, or a mutant alien.

After finding what he could on public resources about the hero, Stark turned to SHIELD. He knew that they would be watching the masked arachnid and hoped that they would have a sufficient amount of information. It took him less than fifteen minutes to hack into the SHIELD data core and even less time to find the file on Spider-Man. Tony was not surprised on what the secret organization had found out about the web-slinging man. He was shocked however to find out that Spider-man was a kid, no more than seventeen. Wrapped up in his thoughts, Tony did not notice a dark man with an eye patch enter the top floor of the Stark building.

"You know Stark, we can detect when and where people hack us." The visitor said. Tony did not turn around, knowing who his guest was.

"You know, I can detect when and where people bypass my security system," Stark retorted, finally turning looking up from his holographic technology. Walking over to the large kitchen part of the open concept apartment, he pulled out two glasses and started making drinks.

"What can I do you for Director." Tony asked after finishing the drinks and walking over to where the Director and decided to stand; near the windowed wall, staring out over the ever-lit city of New York. Tony handed Fury the drink, who took it silently. Tony took a sip from his drink, his mind reeling while he attempted to figure out why this man was here.

"I need a favor Stark. We need Spider-Man on our side, but we need to introduce him to the system discreetly," Fury said, taking a sip from his drink. Recognition filled the eyes of the billionaire-playboy-philanthropist.

"You want me to offer him a job here, at the tower." Tony had, admittedly already thought about the idea.

"Essentially, yes. We want to get close to the boy, but we want him to trust us. If we were to simply show up to his doorstep, he would not I've us any of the information we need. This is a delicate situation and we need his trust." Fury explained, turning to Stark and looking him in the eyes, trying to get him to understand.

"You don't just want him to join the Avengers do you, you want Richards research." Tony more stated that asked.

"Yes." Fury answered. His drink done, he turned to Tony.

"I'm glad we can count on you Stark, let us know when he starts will you, we need to know his every move." Fury said, handing Tony his glass. Tony turned to put the glasses away, and by the time he turned back, Fury was gone.

* * *

Kahtlyn awoke quickly, gasping for breath as if she had just run a marathon. Bright, white, fluorescent lights blinded her eyes. Once her vision cleared, she was able to make out her surroundings. She was in an empty medical room of some sort. There were many different pieces of computerized equipment that were completely foreign to her. Soon, she noticed that she was on sitting on a metal operating table. She was clothed in an ugly blue medical gown. She was hooked up to an IV drip as well as a heart monitor.

Kathlyn's heart beat picked up pace, as indicated by the annoying beeping of the monitor. She had no idea where she was or how she had gotten there. The last thing she remembered was reading a book in her room. Pulling her legs up to her chest, Kathlyn tried hard to keep the panic she was feeling maintained.

The automatic doors on the far side of the room slid open and in walked a man in a lab coat who had his head down as he was flipping through a chart. Looking up, he noticed Kathlyn and smiled.

"Oh good," He said. "You finally awake. We need to run a few more tests, then someone will need to ask you some questions. In the mean time, I will be your doctor, Dr Anderson."


End file.
